Introduction bbb

1. Conserved features of protein-DNA interaction in all X-ray characterized families of DNA-binding proteins N.N. (GI/MR/M) / N.N. (GI/MR/M) ProkaryoticDNA-bendingprotein DNA repair protein MutS, domain I AND • Minor groove: • Helices • Helices +Loops • Sheets + Loops • Helices + Sheets +Loops • Loops • Major groove: • 14,15,16,17,18) Any element 1owf_A 1w7a_A2-116 "Histone-like" proteins from Archaea TATA-box binding protein (TBP), C-terminal domain 1cdw_A155-252 1azp_A Introduction bbb Introduction At the moment more than 1500 structures of protein-DNA complexes are available. Among them there are complexes with proteins that specifically or non-specifically interact with DNA. Proteins interact with DNA in different ways: using helixes, sheets, strands and turns of protein; via major/minor groove, sugar-phosphate backbone of DNA; different combinations of interactions are possible. Development of approaches in systematization of protein-DNA complexes is necessary for understanding mechanisms of protein-DNA interaction.  Results In our group, Nucleic Acid – Protein Interaction DataBase (NPIDB; Spirin,S. et.al. Bioinformatics 2007, 23 (23):3247-8) was created. NPIDB contains 2 747 structures of DNA-protein and RNA-protein complexes supported with search, navigation and analysis tools. For each structure from NPIDB it is possible to download the PDB-structure, find hydrophobic clusters, hydrogen bonds, potential water bridges between protein and DNA; view sequence, view the 3D structure in Jmol, explore link to Pfam and SCOP [fig.1]. Systematization of structural data is performed by classification of protein-DNA interactions. As units of classification, we used structural SCOP (release 1.73, November 2007) domains {fig2}. Basing on interacting elements of protein (helix, sheet, strand, turn) and DNA (the major/minor groove, sugar-phosphate backbone), 20 types of protein-DNA interaction were suggested [fig.3]. Specific contacts and the type of protein-DNA interaction are determined for each DNA-binding protein [fig.4]. Also 110 SCOP domain families containing more than one structure of protein in contact with DNA in PDB files were characterized. For each family, a sequence alignment and a structural alignment were constructed; conserved features including conserved protein-DNA interaction were identified [fig.2]. Figure1 Nucleic Acid – Protein Interaction DataBase Figure3 Classification of protein-DNA interactions Types of protein-DNA interaction Examples of some types of protein-DNA interaction Distribution of SCOP families number in each type Figure 2 SCOP familycharacteristic Figure 4 Type example b-sheetin minor groove • Summary & Outlook • All 110 well-represented by structural data protein domain families were characterized and conserved features were identified. Proposed classification into types of protein-DNA interaction allows revealing specific features of interaction with DNA within protein families. • The results are included into NPIDB. Thus, NPIDB provides users with comprehensive information on structural features of protein domains interacting with DNA. Review of types of protein-DNA interactions basing on the obtained information will be done in forthcoming publication. • All these results are publicly available at NPIDB site (http://mouse.belozersky.msu.su/NPIDB/index.html)